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IPython Interactive Computing and Visualization Cookbook
IPython Interactive Computing and Visualization Cookbook

IPython Interactive Computing and Visualization Cookbook: Over 100 hands-on recipes to sharpen your skills in high-performance numerical computing and data science in the Jupyter Notebook , Second Edition

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IPython Interactive Computing and Visualization Cookbook

Chapter 2. Best Practices in Interactive Computing

In this chapter, we will cover the following topics:

  • Learning the basics of the Unix shell

  • Using the latest features of Python 3

  • Learning the basics of the distributed version control system Git

  • A typical workflow with Git branching

  • Efficient interactive computing workflows with IPython

  • Ten tips for conducting reproducible interactive computing experiments

  • Writing high-quality Python code

  • Writing unit tests with pytest

  • Debugging code with IPython

Introduction


This is a special chapter about good practices in interactive computing. It describes how to work efficiently and properly with the tools this book is about. We will introduce common tools such as the Unix shell, the latest features of Python 3, and Git, before tackling reproducible computing experiments (notably with the Jupyter Notebook).

We will also cover more general topics in software development, such as code quality, debugging, and testing. Attention to these subjects can greatly improve the quality of our end products (for example, software, research, and publications). We will only scratch the surface here, but you will find many references to learn more about these important topics.

Learning the basics of the Unix shell


Learning how to interact with the operating system using a command-line interface (or Terminal) is a required skill in interactive computing and data analysis. We will use a command-line interface in most of the recipes in this book. IPython and the Jupyter Notebook are typically launched from a Terminal. Installing Python packages is typically done from a Terminal.

In this recipe, we will show the very basics of the Unix shell, which is natively available in Linux distributions (such as Debian, Ubuntu, and so on) and macOS. On Windows 10, one can install the Windows Subsystem for Linux, a command-line interface to a Unix subsystem integrated with the Windows operating system (see https://docs.microsoft.com/windows/wsl/about).

Getting ready

Here are the instructions to open a Unix shell on macOS, Linux, and Windows. Bash is the most common Unix shell and this is what we will use in this recipe.

On macOS, bring up the Spotlight Search, type terminal, and...

Using the latest features of Python 3


The latest version of the Python 2.x branch, Python 2.7, was released in 2010. It will reach its end of life in 2020. On the other hand, the first version of the Python 3.x branch, Python 3.0, was released in 2008. The decade-long transition period between Python 2 and Python 3, which are slightly incompatible, has been somewhat chaotic.

Choosing between Python 2 (also known as Legacy Python) and Python 3 used to be tricky since many Python users had not transitioned to Python 3 yet, and many libraries were only compatible with Python 2. Those times are gone and it is now safe to stick with Python 3 in virtually all cases. The only exceptions are when you have to support old unmaintained libraries, or when your users cannot transition to Python 3 for whatever reason.

In addition to fixing the bugs and annoyances of Python 2 (for example, related to Unicode support), Python 3 brings many interesting features in terms of syntax, capabilities of the language...

Learning the basics of the distributed version control system Git


Using a version control system is an absolute requirement in programming and research. This is the tool that makes it just about impossible to lose one's work. In this recipe, we will cover the basics of Git.

Getting ready

Notable distributed version control systems include Git, Mercurial, and Bazaar, among others. In this chapter, we will use the popular Git system. You can download the Git program and Git GUI clients from http://git-scm.com.

Note

Distributed systems tend to be more popular than centralized systems such as SVN or CVS. Distributed systems allow local (offline) changes and offer more flexible collaboration systems.

An online provider allows you to host your code in the cloud. You can use it as a backup of your work and as a platform to share your code with your colleagues. These services include GitHub (https://github.com), GitLab (https://gitlab.com), and Bitbucket (https://bitbucket.org). All of these websites...

A typical workflow with Git branching


A distributed version control system such as Git is designed for the complex and nonlinear workflows that are typical in interactive computing and exploratory research. A central concept is branching, which we will discuss in this recipe.

Getting ready

You need to work in a local Git repository for this recipe (see the previous recipe, Learning the basics of the distributed version control system Git).

How to do it...

  1. We go to the myproject repository and we create a new branch named newidea:

    $ pwd
    /home/cyrille/git/cookbook-2nd/chapter02
    $ cd myproject
    $ git branch newidea
    $ git branch
    * master
      newidea
    

    As indicated by the star *, we are still on the master branch.

  2. We switch to the newly-created newidea branch:

    $ git checkout newidea
    Switched to branch 'newidea'
    $ git branch
      Master
    * newidea
    
  3. We make changes to the code, for instance, by creating a new file:

    $ echo "print('new')" > newfile.py
    $ cat newfile.py
    print('new')
    
  4. We add this file to the staging...

Efficient interactive computing workflows with IPython


There are multiple ways of using IPython for interactive computing. Some of them are better in terms of flexibility, modularity, reusability, and reproducibility. We will review and discuss them in this recipe.

Any interactive computing workflow is based on the following cycle:

  1. Write some code

  2. Execute it

  3. Interpret the results

  4. Repeat

This fundamental loop (also known as Read-Eval-Print Loop (REPL)) is particularly useful when doing exploratory research on data or model simulations, or when building a complex algorithm step by step. A more classical workflow (the edit-compile-run-debug loop) would consist of writing a full-blown program, and then performing a complete analysis. This is generally more tedious. It is more common to build an algorithmic solution iteratively, by doing small-scale experiments and tweaking the parameters, and this is precisely what interactive computing is about.

Integrated Development Environments (IDEs), providing...

Ten tips for conducting reproducible interactive computing experiments


In this recipe, we present ten tips that can help you conduct efficient and reproducible interactive computing experiments. These are more guidelines than absolute rules.

First, we will show how you can improve your productivity by minimizing the time spent doing repetitive tasks and maximizing the time spent thinking about your core work.

Second, we will demonstrate how you can achieve more reproducibility in your computing work. Notably, academic research requires experiments to be reproducible so that any result or conclusion can be verified independently by other researchers. It is not uncommon for errors or manipulations in methods to result in erroneous conclusions that can have damaging consequences. For example, in the 2010 research paper in economics Growth in a Time of Debt, by Carmen Reinhart and Kenneth Rogoff, computational errors were partly responsible for a flawed study with global ramifications for policy...

Writing high-quality Python code


Writing code is easy. Writing high-quality code is much harder. Quality is to be understood both in terms of actual code (variable names, comments, docstrings, and so on) and architecture (functions, modules, and classes). In general, coming up with a well-designed code architecture is much more challenging than the implementation itself.

In this recipe, we will give a few tips about how to write high-quality code. This is a particularly important topic in academia, as more and more scientists without prior experience in software development need to code.

How to do it...

  1. Take the time to learn the Python language seriously. Review the list of all modules in the standard library—you may discover that functions you implemented already exist. Learn to write Pythonic code, and do not translate programming idioms from other languages such as Java or C++ to Python.

  2. Learn common design patterns; these are general reusable solutions to commonly occurring problems in...

Writing unit tests with pytest


Untested code is broken code. Manual testing is essential to ensuring that our software works as expected and does not contain critical bugs. However, manual testing is severely limited because bugs may be introduced at any time in the code.

Nowadays, automated testing is a standard practice in software engineering. In this recipe, we will briefly cover important aspects of automated testing: unit tests, test-driven development, test coverage, and continuous integration. Following these practices is fundamental in order to produce high-quality software.

Getting ready

Python has a native unit testing module that you can readily use (unittest). Other third-party unit testing packages exist. In this recipe, we will use pytest. It is installed by default in Anaconda, but you can also install it manually with conda install pytest.

How to do it...

  1. Let's write in a first.py file a simple function that returns the first element of a list:

    >>> %%writefile first.py...

Debugging code with IPython


Debugging is an integral part of software development and interactive computing. A widespread debugging technique consists of placing the print() functions in various places in the code. Who hasn't done this? It is probably the simplest solution, but it is certainly not the most efficient (it is the poor man's debugger).

IPython is perfectly adapted for debugging, and the integrated debugger is quite easy to use (actually, IPython merely offers a nice interface to the native Python debugger pdb). In particular, tab completion works in the IPython debugger. This recipe describes how to debug code with IPython.

How to do it...

There are two not-mutually exclusive ways of debugging code in Python. In the post-mortem mode, the debugger steps into the code as soon as an exception is raised, so that we can investigate what caused it. In the step-by-step mode, we can stop the interpreter at a breakpoint and resume its execution step by step. This process allows us to check...

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Key benefits

  • • Leverage the Jupyter Notebook for interactive data science and visualization
  • • Become an expert in high-performance computing and visualization for data analysis and scientific modeling
  • • A comprehensive coverage of scientific computing through many hands-on, example-driven recipes with detailed, step-by-step explanations

Description

Python is one of the leading open source platforms for data science and numerical computing. IPython and the associated Jupyter Notebook offer efficient interfaces to Python for data analysis and interactive visualization, and they constitute an ideal gateway to the platform. IPython Interactive Computing and Visualization Cookbook, Second Edition contains many ready-to-use, focused recipes for high-performance scientific computing and data analysis, from the latest IPython/Jupyter features to the most advanced tricks, to help you write better and faster code. You will apply these state-of-the-art methods to various real-world examples, illustrating topics in applied mathematics, scientific modeling, and machine learning. The first part of the book covers programming techniques: code quality and reproducibility, code optimization, high-performance computing through just-in-time compilation, parallel computing, and graphics card programming. The second part tackles data science, statistics, machine learning, signal and image processing, dynamical systems, and pure and applied mathematics.

Who is this book for?

This book is intended for anyone interested in numerical computing and data science: students, researchers, teachers, engineers, analysts, and hobbyists. A basic knowledge of Python/NumPy is recommended. Some skills in mathematics will help you understand the theory behind the computational methods.

What you will learn

  • • Master all features of the Jupyter Notebook
  • • Code better: write high-quality, readable, and well-tested programs; profile and optimize your code; and conduct reproducible interactive computing experiments
  • • Visualize data and create interactive plots in the Jupyter Notebook
  • • Write blazingly fast Python programs with NumPy, ctypes, Numba, Cython, OpenMP, GPU programming (CUDA), parallel IPython, Dask, and more
  • • Analyze data with Bayesian or frequentist statistics (Pandas, PyMC, and R), and learn from actual data through machine learning (scikit-learn)
  • • Gain valuable insights into signals, images, and sounds with SciPy, scikit-image, and OpenCV
  • • Simulate deterministic and stochastic dynamical systems in Python
  • • Familiarize yourself with math in Python using SymPy and Sage: algebra, analysis, logic, graphs, geometry, and probability theory
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Table of Contents

15 Chapters
A Tour of Interactive Computing with Jupyter and IPython Chevron down icon Chevron up icon
Best Practices in Interactive Computing Chevron down icon Chevron up icon
Mastering the Jupyter Notebook Chevron down icon Chevron up icon
Profiling and Optimization Chevron down icon Chevron up icon
High-Performance Computing Chevron down icon Chevron up icon
Data Visualization Chevron down icon Chevron up icon
Statistical Data Analysis Chevron down icon Chevron up icon
Machine Learning Chevron down icon Chevron up icon
Numerical Optimization Chevron down icon Chevron up icon
Signal Processing Chevron down icon Chevron up icon
Image and Audio Processing Chevron down icon Chevron up icon
Deterministic Dynamical Systems Chevron down icon Chevron up icon
Stochastic Dynamical Systems Chevron down icon Chevron up icon
Graphs, Geometry, and Geographic Information Systems Chevron down icon Chevron up icon
Symbolic and Numerical Mathematics Chevron down icon Chevron up icon

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User0910 May 13, 2020
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Le livre va bien au-delà d'IPython et semble en fait s'adresser au scientifique ayant déjà une pratique de python en lui proposant de mettre à jour ses connaissances sur l'écosystème de Python gravitant en gros autour du calcul numérique.Dans l'absolu, le livre est un peu touche à tout, balayant un nombre impressionnant de librairies en 500 pages, là où une seule pourrait faire l'objet d'un livre séparé. D'ordinaire, ce genre d'inventaire à la Prévert a le don d'agacer pour qui n'aime pas le survol.Or ici, un miracle se produit. Peut-être suis-je exactement le lecteur ciblé par l'auteur, mais quasiment chaque section de chaque chapitre fait mouche. Bien qu'utilisant python régulièrement pour mon travail, je m'aperçois à quel point je reste prisonnier des outils que je connais, et combien je suis ignorant de l'incroyable richesse de l'écosystème scientifique et computationel de python.Je n'ai tout simplement jamais mis la main sur un livre contenant une telle densité informative. Bien sûr, aucun sujet n'est réellement approfondi, mais le plus souvent, les librairies ne sont pas simplement mentionnées, mais utilisées dans un exemple informatif qui met le pied à l'étrier.Chapeau à l'auteur pour ses connaissances et sa maîtrise qui transpirent à chaque page de ce livre impressionnant.
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Carol Willing Feb 19, 2018
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The "Cookbook" update adds new content about Jupyter and Python 3.6. It provides a comprehensive, yet understandable, reference to Jupyter, IPython, and frequently used Python data science libraries. The code examples clearly demonstrate how to use popular Python libraries with IPython and Jupyter. Each section contains links to additional resources and provides the reader a wealth of high-quality tips and use cases.I highly recommend the "Cookbook" to people getting started with IPython/Jupyter. The examples and content will also delight current users of IPython/Jupyter. An industry standard, the "Cookbook", is now even better with additional content, updates, and color available for visualizations.
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gary d. smith Jul 28, 2018
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Excellent for my needs as a beginner with Jupyter. very well written. definitely recommend.
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Ken Oct 23, 2019
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The first half of the first chapter was great, the last two sections hard to understand, the second chapter was good. Will update after finished whole book.
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David E. Jun 04, 2018
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Very informative cookbook on IPython.
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